2025-01-16T07:52:34,313 Created temporary directory: /tmp/pip-build-tracker-j7bs27nz 2025-01-16T07:52:34,314 Initialized build tracking at /tmp/pip-build-tracker-j7bs27nz 2025-01-16T07:52:34,314 Created build tracker: /tmp/pip-build-tracker-j7bs27nz 2025-01-16T07:52:34,315 Entered build tracker: /tmp/pip-build-tracker-j7bs27nz 2025-01-16T07:52:34,316 Created temporary directory: /tmp/pip-wheel-39a0i8gb 2025-01-16T07:52:34,320 Created temporary directory: /tmp/pip-ephem-wheel-cache-edgyjoo5 2025-01-16T07:52:34,365 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-01-16T07:52:34,368 2 location(s) to search for versions of protenix: 2025-01-16T07:52:34,368 * https://pypi.org/simple/protenix/ 2025-01-16T07:52:34,368 * https://www.piwheels.org/simple/protenix/ 2025-01-16T07:52:34,368 Fetching project page and analyzing links: https://pypi.org/simple/protenix/ 2025-01-16T07:52:34,369 Getting page https://pypi.org/simple/protenix/ 2025-01-16T07:52:34,371 Found index url https://pypi.org/simple/ 2025-01-16T07:52:34,589 Fetched page https://pypi.org/simple/protenix/ as application/vnd.pypi.simple.v1+json 2025-01-16T07:52:34,597 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/a8/ea/bbe375d1a89b5e3cbe5e07e56184e29a7b779f964a8ea910337a0746af5e/Protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-01-16T07:52:34,598 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/35/f6/105b3517490c13d23880689ef3b4477d072d117ca4cc6f805bad9ee16391/protenix-0.0.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) 2025-01-16T07:52:34,598 Found link https://files.pythonhosted.org/packages/63/d5/22a2098752b2b8c95f2ced18d38918883aa9a5ac8cee9df5174aadfee19c/protenix-0.0.1.tar.gz (from https://pypi.org/simple/protenix/), version: 0.0.1 2025-01-16T07:52:34,599 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/85/33/10bb83edcf222b7cd05cc94d453ac7edfa86f09c7100db8c62fcc894745c/protenix-0.1.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,600 Found link https://files.pythonhosted.org/packages/d5/61/cdea4397a181ca2b108c6df0aa4c30e7a6fc34c5b75ad69557569c44b61d/protenix-0.1.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.0 2025-01-16T07:52:34,601 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/28/00/2206a6a3a02d45eeb6e16c6ffcacff6789f11489238acd07ad5127219741/protenix-0.1.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,602 Found link https://files.pythonhosted.org/packages/2b/7b/20fe2818e890f5d25a892ba31a24b910d0cf34e9f86b990c042c3f91fd05/protenix-0.1.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.1 2025-01-16T07:52:34,602 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/f5/3f/993181bd5478dccf62a5265df701cc9762d257ac04ea6aec26f2e0ec6b0e/protenix-0.1.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10) 2025-01-16T07:52:34,604 Found link https://files.pythonhosted.org/packages/18/ff/8a30b1df6d1bc731a8b4075a077421e306d85976cae82e758a5f15cef4fd/protenix-0.1.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:<3.12,>=3.10), version: 0.1.2 2025-01-16T07:52:34,604 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c3/31/3b2b20aafa4471bcda6389257ad5348c7762374fe725b0552f836dc13ef6/protenix-0.1.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,605 Found link https://files.pythonhosted.org/packages/2c/1c/0788760bb4cd6bae9edc74ef1341e9cc74ad6190b8b5dbd972a361184b97/protenix-0.1.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.1.3 2025-01-16T07:52:34,606 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/09/b7/15a72afe3d229492604e5ca7ebed72cd1402068f2d5518e26ebef3f2bb5c/protenix-0.2.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,607 Found link https://files.pythonhosted.org/packages/0f/17/fdc141be77d735ddf3bfba80a660873fa13732b6c77847434b969aa66f51/protenix-0.2.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.2.0 2025-01-16T07:52:34,608 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/99/56/de0a35a125cc0247a366608c8598bdd949ba6068c02fb8d13e8147f65d9c/protenix-0.3.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,608 Found link https://files.pythonhosted.org/packages/b6/96/8d6d036dcaff9c1884fcbaa2c752fed65e24320fab2a0a8b128a615da89d/protenix-0.3.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.0 2025-01-16T07:52:34,609 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/bf/6b/1cb9d8eea4be4973f97bd1f138f6da0711fad309b76b5c977b316c6bc511/protenix-0.3.1-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,610 Found link https://files.pythonhosted.org/packages/9a/85/b1ec219c8b8a3ba735742164561a917f53e81f11d2a3a9544a206f9ac21b/protenix-0.3.1.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.1 2025-01-16T07:52:34,610 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/6d/11/4c2946b935b56d995c7418cfc783c16e9e647de72a34380c42e573d4b28d/protenix-0.3.2-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,611 Found link https://files.pythonhosted.org/packages/65/48/25fdef4629cd5ce68c65f733fc49388378cacd3658cd76b5e88893ca5227/protenix-0.3.2.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.2 2025-01-16T07:52:34,612 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/c7/93/f19c14b2b49405f326fab9594ffd7252ef0e231cc348d61b5e406408c8cf/protenix-0.3.3-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,613 Found link https://files.pythonhosted.org/packages/83/67/8697c13e89ed881756f1d188346b4e241decea92545f611778baa9273a49/protenix-0.3.3.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.3 2025-01-16T07:52:34,614 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/49/29/b5b7a2e6e0802ba1d6256d774aafcce43d86773202697a4d1ebb7ff3a95a/protenix-0.3.4-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,614 Found link https://files.pythonhosted.org/packages/67/bf/6ccce5f88c48f27559d138e5b4e65170e318a0d97c803c655ba3734f9efd/protenix-0.3.4.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.4 2025-01-16T07:52:34,615 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/22/4e/6387baad87ace43b71024601db621c8adb12645ee898bfdf653ffe0067d5/protenix-0.3.5-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,616 Found link https://files.pythonhosted.org/packages/8e/75/ba5a8e3b5e13eab23909185b11b044e4e3db04ade55485e9d7fe09b6e95e/protenix-0.3.5.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.5 2025-01-16T07:52:34,617 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/13/c0/5653f9f3db2450d9c2508c32bccf1503610ef34da8d8d10921db6a750635/protenix-0.3.6-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,618 Found link https://files.pythonhosted.org/packages/02/16/6482a30fa395df9360f808fe44260a9513abff61efdd75f671a7556028eb/protenix-0.3.6.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.6 2025-01-16T07:52:34,618 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/01/68/a09d38d3fc22f34ba7a914f9863ae9b7f2c77f4bfb8fe275aabd477cffa6/protenix-0.3.7-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,620 Found link https://files.pythonhosted.org/packages/fe/58/241e5813c71a2f8d427f579892c69507b4b132537f332faf24f64ebddbc1/protenix-0.3.7.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.7 2025-01-16T07:52:34,620 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/be/4d/3a2a007bfb6bab07c98ec53180368db69bd656a3ee277a6a962068da3b06/protenix-0.3.8-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,621 Found link https://files.pythonhosted.org/packages/1f/aa/2445a83be220fc2a24fd269f34dfbfa2e5c9d025103712070bfc85d9bb3f/protenix-0.3.8.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.8 2025-01-16T07:52:34,622 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/2e/8c/93ac8551d47bd1189977231ce255647b3b86d727d67c9ed7e756215aea3a/protenix-0.3.9-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,622 Found link https://files.pythonhosted.org/packages/57/c4/d9f0a75ae91d1d017c3a3375a9f65ea08165b9123647f085c9d3f8835e36/protenix-0.3.9.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.3.9 2025-01-16T07:52:34,623 Skipping link: No binaries permitted for protenix: https://files.pythonhosted.org/packages/53/b4/bc84d60b3c57955f15cb920f570b1f0a0b3248325099a3b4fc4db7c574b3/protenix-0.4.0-py3-none-any.whl (from https://pypi.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,624 Found link https://files.pythonhosted.org/packages/e9/82/57b5b8cdcfc8221b69016228934083fc0ea2174dbe398e364069b28d88c7/protenix-0.4.0.tar.gz (from https://pypi.org/simple/protenix/) (requires-python:>=3.10), version: 0.4.0 2025-01-16T07:52:34,625 Fetching project page and analyzing links: https://www.piwheels.org/simple/protenix/ 2025-01-16T07:52:34,626 Getting page https://www.piwheels.org/simple/protenix/ 2025-01-16T07:52:34,627 Found index url https://www.piwheels.org/simple/ 2025-01-16T07:52:34,818 Fetched page https://www.piwheels.org/simple/protenix/ as text/html 2025-01-16T07:52:34,824 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.9-py3-none-any.whl#sha256=86574af5793f00ee12318cfba832f84252f41b928767e598c3a817a9f1c85ae3 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,824 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.8-py3-none-any.whl#sha256=f48473ae65c65269825258d1076bd926d822c91535ffc1016ec1b6aa051d6c12 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,825 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.7-py3-none-any.whl#sha256=879dd062411f30d5ec9abcb895ee06a2acd7c7435135ea457af7d665e7351ed5 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,826 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.6-py3-none-any.whl#sha256=a740708421da6bea03c22fc527e96ec0ce27329a9cfb8adb213d0ad1ec66d031 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,826 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.5-py3-none-any.whl#sha256=3719630079eefd5a0ef318cdb45dae22c0b16dd3c6b29bbfcd3b175aa939770b (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,827 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.4-py3-none-any.whl#sha256=d375e6e6506082ba1ef1e01d816c701e9287af557cb0852c45aea426702f052f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,827 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.3-py3-none-any.whl#sha256=bce00ef75c8d8f408dca3bd0105c8bc555da5e34c8998748544be1bb5f763c02 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,828 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.2-py3-none-any.whl#sha256=0255f130567cda78b0dd7e9e1efee966d489a4302df91f47c2ce7d7c5f9b3400 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,829 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.1-py3-none-any.whl#sha256=624b9eaf9450baa3748fbe7d038a393ab59d36d7b191a70d676d592c81f46d1f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,829 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.3.0-py3-none-any.whl#sha256=c2af82dfdebc9606f320eb2d0ae308e644cd77922b443dcd59e7f778e756ac45 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,829 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.2.0-py3-none-any.whl#sha256=0de87030b4ba1d9e3c2b67265493001f00eca096d862816f65f818b739c96c6f (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,830 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.3-py3-none-any.whl#sha256=be21c60c572799c5562933a71a3087ae1441533805771913e77578fc6280e314 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,830 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.2-py3-none-any.whl#sha256=10909020be81638dbfe8da0ff0bc107ad732dc3dc8e420d09aa3e346c53ac527 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10,<3.12) 2025-01-16T07:52:34,831 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.1-py3-none-any.whl#sha256=aa7a8c0ad8f38f5430cb145bb56675e2b0deb861589bbb05ec6eb09dd95c5f57 (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,831 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/protenix-0.1.0-py3-none-any.whl#sha256=95dd14c125ff66c76135ed8525ede80d6be803880749ec813036bb317ca23e6e (from https://www.piwheels.org/simple/protenix/) (requires-python:>=3.10) 2025-01-16T07:52:34,832 Skipping link: No binaries permitted for protenix: https://www.piwheels.org/simple/protenix/Protenix-0.0.1-py3-none-any.whl#sha256=5b251c54ef00f26ee302a294be031208ca73350e41e88d05368f4146cdb01794 (from https://www.piwheels.org/simple/protenix/) 2025-01-16T07:52:34,833 Skipping link: not a file: https://www.piwheels.org/simple/protenix/ 2025-01-16T07:52:34,833 Skipping link: not a file: https://pypi.org/simple/protenix/ 2025-01-16T07:52:34,854 Given no hashes to check 1 links for project 'protenix': discarding no candidates 2025-01-16T07:52:34,856 Collecting protenix==0.4.0 2025-01-16T07:52:34,859 Created temporary directory: /tmp/pip-unpack-fj8nd974 2025-01-16T07:52:35,000 Downloading protenix-0.4.0.tar.gz (339 kB) 2025-01-16T07:52:35,419 Added protenix==0.4.0 from https://files.pythonhosted.org/packages/e9/82/57b5b8cdcfc8221b69016228934083fc0ea2174dbe398e364069b28d88c7/protenix-0.4.0.tar.gz to build tracker '/tmp/pip-build-tracker-j7bs27nz' 2025-01-16T07:52:35,422 Running setup.py (path:/tmp/pip-wheel-39a0i8gb/protenix_78c302e1732e4208b97125152f624044/setup.py) egg_info for package protenix 2025-01-16T07:52:35,423 Created temporary directory: /tmp/pip-pip-egg-info-u6wu0mt5 2025-01-16T07:52:35,424 Preparing metadata (setup.py): started 2025-01-16T07:52:35,425 Running command python setup.py egg_info 2025-01-16T07:52:36,543 running egg_info 2025-01-16T07:52:36,571 creating /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info 2025-01-16T07:52:36,572 writing /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/PKG-INFO 2025-01-16T07:52:36,575 writing dependency_links to /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/dependency_links.txt 2025-01-16T07:52:36,576 writing entry points to /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/entry_points.txt 2025-01-16T07:52:36,578 writing requirements to /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/requires.txt 2025-01-16T07:52:36,579 writing top-level names to /tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/top_level.txt 2025-01-16T07:52:36,581 writing manifest file '/tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/SOURCES.txt' 2025-01-16T07:52:36,691 reading manifest file '/tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/SOURCES.txt' 2025-01-16T07:52:36,693 adding license file 'LICENSE' 2025-01-16T07:52:36,699 writing manifest file '/tmp/pip-pip-egg-info-u6wu0mt5/protenix.egg-info/SOURCES.txt' 2025-01-16T07:52:36,808 Preparing metadata (setup.py): finished with status 'done' 2025-01-16T07:52:36,812 Source in /tmp/pip-wheel-39a0i8gb/protenix_78c302e1732e4208b97125152f624044 has version 0.4.0, which satisfies requirement protenix==0.4.0 from https://files.pythonhosted.org/packages/e9/82/57b5b8cdcfc8221b69016228934083fc0ea2174dbe398e364069b28d88c7/protenix-0.4.0.tar.gz 2025-01-16T07:52:36,813 Removed protenix==0.4.0 from https://files.pythonhosted.org/packages/e9/82/57b5b8cdcfc8221b69016228934083fc0ea2174dbe398e364069b28d88c7/protenix-0.4.0.tar.gz from build tracker '/tmp/pip-build-tracker-j7bs27nz' 2025-01-16T07:52:36,822 Created temporary directory: /tmp/pip-unpack-rix6al9x 2025-01-16T07:52:36,823 Created temporary directory: /tmp/pip-unpack-jtbqmvo1 2025-01-16T07:52:36,824 Building wheels for collected packages: protenix 2025-01-16T07:52:36,828 Created temporary directory: /tmp/pip-wheel-6man6dli 2025-01-16T07:52:36,828 Building wheel for protenix (setup.py): started 2025-01-16T07:52:36,829 Destination directory: /tmp/pip-wheel-6man6dli 2025-01-16T07:52:36,830 Running command python setup.py bdist_wheel 2025-01-16T07:52:37,867 running bdist_wheel 2025-01-16T07:52:38,001 running build 2025-01-16T07:52:38,002 running build_py 2025-01-16T07:52:38,032 creating build/lib/scripts 2025-01-16T07:52:38,035 copying scripts/prepare_training_data.py -> build/lib/scripts 2025-01-16T07:52:38,037 copying scripts/__init__.py -> build/lib/scripts 2025-01-16T07:52:38,039 copying scripts/gen_ccd_cache.py -> build/lib/scripts 2025-01-16T07:52:38,042 copying scripts/colabfold_msa.py -> build/lib/scripts 2025-01-16T07:52:38,045 creating build/lib/runner 2025-01-16T07:52:38,046 copying runner/__init__.py -> build/lib/runner 2025-01-16T07:52:38,047 copying runner/inference.py -> build/lib/runner 2025-01-16T07:52:38,050 copying runner/batch_inference.py -> build/lib/runner 2025-01-16T07:52:38,053 copying runner/ema.py -> build/lib/runner 2025-01-16T07:52:38,055 copying runner/dumper.py -> build/lib/runner 2025-01-16T07:52:38,057 copying runner/train.py -> build/lib/runner 2025-01-16T07:52:38,060 copying runner/msa_search.py -> build/lib/runner 2025-01-16T07:52:38,062 creating build/lib/protenix 2025-01-16T07:52:38,063 copying protenix/__init__.py -> build/lib/protenix 2025-01-16T07:52:38,066 creating build/lib/configs 2025-01-16T07:52:38,067 copying configs/__init__.py -> build/lib/configs 2025-01-16T07:52:38,069 copying configs/configs_base.py -> build/lib/configs 2025-01-16T07:52:38,071 copying configs/configs_inference.py -> build/lib/configs 2025-01-16T07:52:38,073 copying configs/configs_data.py -> build/lib/configs 2025-01-16T07:52:38,075 creating build/lib/protenix/config 2025-01-16T07:52:38,077 copying protenix/config/__init__.py -> build/lib/protenix/config 2025-01-16T07:52:38,079 copying protenix/config/extend_types.py -> build/lib/protenix/config 2025-01-16T07:52:38,081 copying protenix/config/config.py -> build/lib/protenix/config 2025-01-16T07:52:38,083 creating build/lib/protenix/web_service 2025-01-16T07:52:38,085 copying protenix/web_service/viewer.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,087 copying protenix/web_service/__init__.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,089 copying protenix/web_service/colab_request_utils.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,091 copying protenix/web_service/prediction_visualization.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,094 copying protenix/web_service/dependency_url.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,095 copying protenix/web_service/colab_request_parser.py -> build/lib/protenix/web_service 2025-01-16T07:52:38,098 creating build/lib/protenix/openfold_local 2025-01-16T07:52:38,099 copying protenix/openfold_local/__init__.py -> build/lib/protenix/openfold_local 2025-01-16T07:52:38,102 creating build/lib/protenix/data 2025-01-16T07:52:38,103 copying protenix/data/msa_featurizer.py -> build/lib/protenix/data 2025-01-16T07:52:38,106 copying protenix/data/__init__.py -> build/lib/protenix/data 2025-01-16T07:52:38,108 copying protenix/data/json_parser.py -> build/lib/protenix/data 2025-01-16T07:52:38,110 copying protenix/data/tokenizer.py -> build/lib/protenix/data 2025-01-16T07:52:38,113 copying protenix/data/parser.py -> build/lib/protenix/data 2025-01-16T07:52:38,117 copying protenix/data/ccd.py -> build/lib/protenix/data 2025-01-16T07:52:38,120 copying protenix/data/substructure_perms.py -> build/lib/protenix/data 2025-01-16T07:52:38,122 copying protenix/data/data_pipeline.py -> build/lib/protenix/data 2025-01-16T07:52:38,125 copying protenix/data/featurizer.py -> build/lib/protenix/data 2025-01-16T07:52:38,127 copying protenix/data/json_maker.py -> build/lib/protenix/data 2025-01-16T07:52:38,130 copying protenix/data/infer_data_pipeline.py -> build/lib/protenix/data 2025-01-16T07:52:38,132 copying protenix/data/json_to_feature.py -> build/lib/protenix/data 2025-01-16T07:52:38,134 copying protenix/data/dataset.py -> build/lib/protenix/data 2025-01-16T07:52:38,137 copying protenix/data/msa_utils.py -> build/lib/protenix/data 2025-01-16T07:52:38,140 copying protenix/data/dataloader.py -> build/lib/protenix/data 2025-01-16T07:52:38,143 copying protenix/data/filter.py -> build/lib/protenix/data 2025-01-16T07:52:38,146 copying protenix/data/constants.py -> build/lib/protenix/data 2025-01-16T07:52:38,149 copying protenix/data/utils.py -> build/lib/protenix/data 2025-01-16T07:52:38,153 creating build/lib/protenix/utils 2025-01-16T07:52:38,154 copying protenix/utils/logger.py -> build/lib/protenix/utils 2025-01-16T07:52:38,156 copying protenix/utils/torch_utils.py -> build/lib/protenix/utils 2025-01-16T07:52:38,158 copying protenix/utils/geometry.py -> build/lib/protenix/utils 2025-01-16T07:52:38,160 copying protenix/utils/training.py -> build/lib/protenix/utils 2025-01-16T07:52:38,162 copying protenix/utils/metrics.py -> build/lib/protenix/utils 2025-01-16T07:52:38,164 copying protenix/utils/__init__.py -> build/lib/protenix/utils 2025-01-16T07:52:38,166 copying protenix/utils/file_io.py -> build/lib/protenix/utils 2025-01-16T07:52:38,168 copying protenix/utils/distributed.py -> build/lib/protenix/utils 2025-01-16T07:52:38,170 copying protenix/utils/cropping.py -> build/lib/protenix/utils 2025-01-16T07:52:38,173 copying protenix/utils/seed.py -> build/lib/protenix/utils 2025-01-16T07:52:38,175 copying protenix/utils/lr_scheduler.py -> build/lib/protenix/utils 2025-01-16T07:52:38,177 copying protenix/utils/scatter_utils.py -> build/lib/protenix/utils 2025-01-16T07:52:38,180 creating build/lib/protenix/metrics 2025-01-16T07:52:38,181 copying protenix/metrics/__init__.py -> build/lib/protenix/metrics 2025-01-16T07:52:38,183 copying protenix/metrics/rmsd.py -> build/lib/protenix/metrics 2025-01-16T07:52:38,186 copying protenix/metrics/lddt_metrics.py -> build/lib/protenix/metrics 2025-01-16T07:52:38,189 copying protenix/metrics/clash.py -> build/lib/protenix/metrics 2025-01-16T07:52:38,192 creating build/lib/protenix/model 2025-01-16T07:52:38,193 copying protenix/model/protenix.py -> build/lib/protenix/model 2025-01-16T07:52:38,196 copying protenix/model/__init__.py -> build/lib/protenix/model 2025-01-16T07:52:38,197 copying protenix/model/loss.py -> build/lib/protenix/model 2025-01-16T07:52:38,201 copying protenix/model/generator.py -> build/lib/protenix/model 2025-01-16T07:52:38,204 copying protenix/model/sample_confidence.py -> build/lib/protenix/model 2025-01-16T07:52:38,206 copying protenix/model/utils.py -> build/lib/protenix/model 2025-01-16T07:52:38,210 creating build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,211 copying protenix/openfold_local/data/data_transforms.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,214 copying protenix/openfold_local/data/msa_pairing.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,216 copying protenix/openfold_local/data/__init__.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,218 copying protenix/openfold_local/data/templates.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,221 copying protenix/openfold_local/data/errors.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,223 copying protenix/openfold_local/data/mmcif_parsing.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,226 copying protenix/openfold_local/data/msa_identifiers.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,228 copying protenix/openfold_local/data/parsers.py -> build/lib/protenix/openfold_local/data 2025-01-16T07:52:38,231 creating build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,233 copying protenix/openfold_local/utils/precision_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,235 copying protenix/openfold_local/utils/feats.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,237 copying protenix/openfold_local/utils/checkpointing.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,239 copying protenix/openfold_local/utils/all_atom_multimer.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,242 copying protenix/openfold_local/utils/__init__.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,244 copying protenix/openfold_local/utils/chunk_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,247 copying protenix/openfold_local/utils/tensor_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,249 copying protenix/openfold_local/utils/rigid_utils.py -> build/lib/protenix/openfold_local/utils 2025-01-16T07:52:38,252 creating build/lib/protenix/openfold_local/np 2025-01-16T07:52:38,253 copying protenix/openfold_local/np/__init__.py -> build/lib/protenix/openfold_local/np 2025-01-16T07:52:38,255 copying protenix/openfold_local/np/residue_constants.py -> build/lib/protenix/openfold_local/np 2025-01-16T07:52:38,258 creating build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,259 copying protenix/openfold_local/model/outer_product_mean.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,262 copying protenix/openfold_local/model/triangular_attention.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,265 copying protenix/openfold_local/model/__init__.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,266 copying protenix/openfold_local/model/dropout.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,268 copying protenix/openfold_local/model/triangular_multiplicative_update.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,271 copying protenix/openfold_local/model/primitives.py -> build/lib/protenix/openfold_local/model 2025-01-16T07:52:38,274 creating build/lib/protenix/openfold_local/data/tools 2025-01-16T07:52:38,275 copying protenix/openfold_local/data/tools/__init__.py -> build/lib/protenix/openfold_local/data/tools 2025-01-16T07:52:38,277 copying protenix/openfold_local/data/tools/jackhmmer.py -> build/lib/protenix/openfold_local/data/tools 2025-01-16T07:52:38,280 copying protenix/openfold_local/data/tools/utils.py -> build/lib/protenix/openfold_local/data/tools 2025-01-16T07:52:38,282 creating build/lib/protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,283 copying protenix/openfold_local/utils/kernel/__init__.py -> build/lib/protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,285 copying protenix/openfold_local/utils/kernel/attention_core.py -> build/lib/protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,287 creating build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,288 copying protenix/openfold_local/utils/geometry/__init__.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,290 copying protenix/openfold_local/utils/geometry/quat_rigid.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,292 copying protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,294 copying protenix/openfold_local/utils/geometry/test_utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,296 copying protenix/openfold_local/utils/geometry/vector.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,298 copying protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,301 copying protenix/openfold_local/utils/geometry/utils.py -> build/lib/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,303 creating build/lib/protenix/utils/permutation 2025-01-16T07:52:38,304 copying protenix/utils/permutation/__init__.py -> build/lib/protenix/utils/permutation 2025-01-16T07:52:38,306 copying protenix/utils/permutation/atom_permutation.py -> build/lib/protenix/utils/permutation 2025-01-16T07:52:38,309 copying protenix/utils/permutation/permutation.py -> build/lib/protenix/utils/permutation 2025-01-16T07:52:38,311 copying protenix/utils/permutation/utils.py -> build/lib/protenix/utils/permutation 2025-01-16T07:52:38,314 creating build/lib/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,315 copying protenix/utils/permutation/chain_permutation/__init__.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,318 copying protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,321 copying protenix/utils/permutation/chain_permutation/heuristic.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,324 copying protenix/utils/permutation/chain_permutation/utils.py -> build/lib/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,326 creating build/lib/protenix/model/modules 2025-01-16T07:52:38,327 copying protenix/model/modules/confidence.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,330 copying protenix/model/modules/transformer.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,333 copying protenix/model/modules/embedders.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,335 copying protenix/model/modules/__init__.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,337 copying protenix/model/modules/diffusion.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,340 copying protenix/model/modules/pairformer.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,343 copying protenix/model/modules/frames.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,345 copying protenix/model/modules/head.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,347 copying protenix/model/modules/primitives.py -> build/lib/protenix/model/modules 2025-01-16T07:52:38,350 creating build/lib/protenix/model/layer_norm 2025-01-16T07:52:38,352 copying protenix/model/layer_norm/__init__.py -> build/lib/protenix/model/layer_norm 2025-01-16T07:52:38,354 copying protenix/model/layer_norm/torch_ext_compile.py -> build/lib/protenix/model/layer_norm 2025-01-16T07:52:38,355 copying protenix/model/layer_norm/layer_norm.py -> build/lib/protenix/model/layer_norm 2025-01-16T07:52:38,357 running egg_info 2025-01-16T07:52:38,387 writing protenix.egg-info/PKG-INFO 2025-01-16T07:52:38,390 writing dependency_links to protenix.egg-info/dependency_links.txt 2025-01-16T07:52:38,392 writing entry points to protenix.egg-info/entry_points.txt 2025-01-16T07:52:38,394 writing requirements to protenix.egg-info/requires.txt 2025-01-16T07:52:38,395 writing top-level names to protenix.egg-info/top_level.txt 2025-01-16T07:52:38,444 reading manifest file 'protenix.egg-info/SOURCES.txt' 2025-01-16T07:52:38,453 adding license file 'LICENSE' 2025-01-16T07:52:38,461 writing manifest file 'protenix.egg-info/SOURCES.txt' 2025-01-16T07:52:38,464 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'protenix.model.layer_norm.kernel' is absent from the `packages` configuration. 2025-01-16T07:52:38,465 !! 2025-01-16T07:52:38,466 ******************************************************************************** 2025-01-16T07:52:38,466 ############################ 2025-01-16T07:52:38,467 # Package would be ignored # 2025-01-16T07:52:38,467 ############################ 2025-01-16T07:52:38,468 Python recognizes 'protenix.model.layer_norm.kernel' as an importable package[^1], 2025-01-16T07:52:38,469 but it is absent from setuptools' `packages` configuration. 2025-01-16T07:52:38,470 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-16T07:52:38,470 package, please make sure that 'protenix.model.layer_norm.kernel' is explicitly added 2025-01-16T07:52:38,471 to the `packages` configuration field. 2025-01-16T07:52:38,472 Alternatively, you can also rely on setuptools' discovery methods 2025-01-16T07:52:38,472 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-16T07:52:38,473 instead of `find_packages(...)`/`find:`). 2025-01-16T07:52:38,474 You can read more about "package discovery" on setuptools documentation page: 2025-01-16T07:52:38,475 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-16T07:52:38,476 If you don't want 'protenix.model.layer_norm.kernel' to be distributed and are 2025-01-16T07:52:38,477 already explicitly excluding 'protenix.model.layer_norm.kernel' via 2025-01-16T07:52:38,477 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-16T07:52:38,478 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-16T07:52:38,478 combination with a more fine grained `package-data` configuration. 2025-01-16T07:52:38,479 You can read more about "package data files" on setuptools documentation page: 2025-01-16T07:52:38,481 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-16T07:52:38,482 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-16T07:52:38,483 even if it does not contain any `.py` files. 2025-01-16T07:52:38,483 On the other hand, currently there is no concept of package data 2025-01-16T07:52:38,484 directory, all directories are treated like packages. 2025-01-16T07:52:38,485 ******************************************************************************** 2025-01-16T07:52:38,486 !! 2025-01-16T07:52:38,486 check.warn(importable) 2025-01-16T07:52:38,487 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'scripts.msa' is absent from the `packages` configuration. 2025-01-16T07:52:38,487 !! 2025-01-16T07:52:38,489 ******************************************************************************** 2025-01-16T07:52:38,489 ############################ 2025-01-16T07:52:38,490 # Package would be ignored # 2025-01-16T07:52:38,490 ############################ 2025-01-16T07:52:38,491 Python recognizes 'scripts.msa' as an importable package[^1], 2025-01-16T07:52:38,491 but it is absent from setuptools' `packages` configuration. 2025-01-16T07:52:38,492 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-16T07:52:38,493 package, please make sure that 'scripts.msa' is explicitly added 2025-01-16T07:52:38,493 to the `packages` configuration field. 2025-01-16T07:52:38,494 Alternatively, you can also rely on setuptools' discovery methods 2025-01-16T07:52:38,495 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-16T07:52:38,495 instead of `find_packages(...)`/`find:`). 2025-01-16T07:52:38,496 You can read more about "package discovery" on setuptools documentation page: 2025-01-16T07:52:38,497 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-16T07:52:38,498 If you don't want 'scripts.msa' to be distributed and are 2025-01-16T07:52:38,499 already explicitly excluding 'scripts.msa' via 2025-01-16T07:52:38,499 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-16T07:52:38,500 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-16T07:52:38,500 combination with a more fine grained `package-data` configuration. 2025-01-16T07:52:38,501 You can read more about "package data files" on setuptools documentation page: 2025-01-16T07:52:38,502 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-16T07:52:38,504 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-16T07:52:38,505 even if it does not contain any `.py` files. 2025-01-16T07:52:38,505 On the other hand, currently there is no concept of package data 2025-01-16T07:52:38,506 directory, all directories are treated like packages. 2025-01-16T07:52:38,506 ******************************************************************************** 2025-01-16T07:52:38,507 !! 2025-01-16T07:52:38,508 check.warn(importable) 2025-01-16T07:52:38,509 creating build/lib/scripts/msa 2025-01-16T07:52:38,509 copying scripts/msa/step1-get_prot_seq.py -> build/lib/scripts/msa 2025-01-16T07:52:38,510 copying scripts/msa/step2-get_msa.ipynb -> build/lib/scripts/msa 2025-01-16T07:52:38,510 copying scripts/msa/step3-uniref_add_taxid.py -> build/lib/scripts/msa 2025-01-16T07:52:38,511 copying scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/lib/scripts/msa 2025-01-16T07:52:38,511 creating build/lib/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,512 copying protenix/model/layer_norm/kernel/compat.h -> build/lib/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,513 copying protenix/model/layer_norm/kernel/type_shim.h -> build/lib/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,513 copying protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/lib/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,514 copying protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/lib/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,551 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-01-16T07:52:38,552 !! 2025-01-16T07:52:38,553 ******************************************************************************** 2025-01-16T07:52:38,554 Please avoid running ``setup.py`` directly. 2025-01-16T07:52:38,554 Instead, use pypa/build, pypa/installer or other 2025-01-16T07:52:38,555 standards-based tools. 2025-01-16T07:52:38,556 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-01-16T07:52:38,557 ******************************************************************************** 2025-01-16T07:52:38,558 !! 2025-01-16T07:52:38,558 self.initialize_options() 2025-01-16T07:52:38,581 installing to build/bdist.linux-armv7l/wheel 2025-01-16T07:52:38,582 running install 2025-01-16T07:52:38,607 running install_lib 2025-01-16T07:52:38,634 creating build/bdist.linux-armv7l/wheel 2025-01-16T07:52:38,636 creating build/bdist.linux-armv7l/wheel/scripts 2025-01-16T07:52:38,637 copying build/lib/scripts/prepare_training_data.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-16T07:52:38,640 copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-16T07:52:38,641 copying build/lib/scripts/gen_ccd_cache.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-16T07:52:38,643 copying build/lib/scripts/colabfold_msa.py -> build/bdist.linux-armv7l/wheel/./scripts 2025-01-16T07:52:38,646 creating build/bdist.linux-armv7l/wheel/scripts/msa 2025-01-16T07:52:38,648 copying build/lib/scripts/msa/step3-uniref_add_taxid.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-16T07:52:38,650 copying build/lib/scripts/msa/step2-get_msa.ipynb -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-16T07:52:38,652 copying build/lib/scripts/msa/step1-get_prot_seq.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-16T07:52:38,654 copying build/lib/scripts/msa/step4-split_msa_to_uniref_and_others.py -> build/bdist.linux-armv7l/wheel/./scripts/msa 2025-01-16T07:52:38,657 creating build/bdist.linux-armv7l/wheel/runner 2025-01-16T07:52:38,658 copying build/lib/runner/__init__.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,659 copying build/lib/runner/inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,662 copying build/lib/runner/batch_inference.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,664 copying build/lib/runner/ema.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,666 copying build/lib/runner/dumper.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,668 copying build/lib/runner/train.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,671 copying build/lib/runner/msa_search.py -> build/bdist.linux-armv7l/wheel/./runner 2025-01-16T07:52:38,674 creating build/bdist.linux-armv7l/wheel/protenix 2025-01-16T07:52:38,676 creating build/bdist.linux-armv7l/wheel/protenix/config 2025-01-16T07:52:38,677 copying build/lib/protenix/config/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-16T07:52:38,679 copying build/lib/protenix/config/extend_types.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-16T07:52:38,681 copying build/lib/protenix/config/config.py -> build/bdist.linux-armv7l/wheel/./protenix/config 2025-01-16T07:52:38,684 creating build/bdist.linux-armv7l/wheel/protenix/web_service 2025-01-16T07:52:38,685 copying build/lib/protenix/web_service/viewer.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,688 copying build/lib/protenix/web_service/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,689 copying build/lib/protenix/web_service/colab_request_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,692 copying build/lib/protenix/web_service/prediction_visualization.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,694 copying build/lib/protenix/web_service/dependency_url.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,696 copying build/lib/protenix/web_service/colab_request_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/web_service 2025-01-16T07:52:38,699 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local 2025-01-16T07:52:38,701 copying build/lib/protenix/openfold_local/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local 2025-01-16T07:52:38,703 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data 2025-01-16T07:52:38,705 copying build/lib/protenix/openfold_local/data/data_transforms.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,707 copying build/lib/protenix/openfold_local/data/msa_pairing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,710 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/data/tools 2025-01-16T07:52:38,711 copying build/lib/protenix/openfold_local/data/tools/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-16T07:52:38,713 copying build/lib/protenix/openfold_local/data/tools/jackhmmer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-16T07:52:38,715 copying build/lib/protenix/openfold_local/data/tools/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data/tools 2025-01-16T07:52:38,718 copying build/lib/protenix/openfold_local/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,719 copying build/lib/protenix/openfold_local/data/templates.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,722 copying build/lib/protenix/openfold_local/data/errors.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,724 copying build/lib/protenix/openfold_local/data/mmcif_parsing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,726 copying build/lib/protenix/openfold_local/data/msa_identifiers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,729 copying build/lib/protenix/openfold_local/data/parsers.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/data 2025-01-16T07:52:38,732 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils 2025-01-16T07:52:38,733 copying build/lib/protenix/openfold_local/utils/precision_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,735 copying build/lib/protenix/openfold_local/utils/feats.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,737 copying build/lib/protenix/openfold_local/utils/checkpointing.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,739 copying build/lib/protenix/openfold_local/utils/all_atom_multimer.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,742 copying build/lib/protenix/openfold_local/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,743 copying build/lib/protenix/openfold_local/utils/chunk_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,746 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,747 copying build/lib/protenix/openfold_local/utils/kernel/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,749 copying build/lib/protenix/openfold_local/utils/kernel/attention_core.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/kernel 2025-01-16T07:52:38,752 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,753 copying build/lib/protenix/openfold_local/utils/geometry/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,755 copying build/lib/protenix/openfold_local/utils/geometry/quat_rigid.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,757 copying build/lib/protenix/openfold_local/utils/geometry/rigid_matrix_vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,759 copying build/lib/protenix/openfold_local/utils/geometry/test_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,761 copying build/lib/protenix/openfold_local/utils/geometry/vector.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,763 copying build/lib/protenix/openfold_local/utils/geometry/rotation_matrix.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,766 copying build/lib/protenix/openfold_local/utils/geometry/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils/geometry 2025-01-16T07:52:38,767 copying build/lib/protenix/openfold_local/utils/tensor_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,769 copying build/lib/protenix/openfold_local/utils/rigid_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/utils 2025-01-16T07:52:38,773 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/np 2025-01-16T07:52:38,774 copying build/lib/protenix/openfold_local/np/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-01-16T07:52:38,776 copying build/lib/protenix/openfold_local/np/residue_constants.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/np 2025-01-16T07:52:38,780 creating build/bdist.linux-armv7l/wheel/protenix/openfold_local/model 2025-01-16T07:52:38,781 copying build/lib/protenix/openfold_local/model/outer_product_mean.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,783 copying build/lib/protenix/openfold_local/model/triangular_attention.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,786 copying build/lib/protenix/openfold_local/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,788 copying build/lib/protenix/openfold_local/model/dropout.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,790 copying build/lib/protenix/openfold_local/model/triangular_multiplicative_update.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,793 copying build/lib/protenix/openfold_local/model/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/openfold_local/model 2025-01-16T07:52:38,795 copying build/lib/protenix/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix 2025-01-16T07:52:38,798 creating build/bdist.linux-armv7l/wheel/protenix/data 2025-01-16T07:52:38,800 copying build/lib/protenix/data/msa_featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,803 copying build/lib/protenix/data/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,805 copying build/lib/protenix/data/json_parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,808 copying build/lib/protenix/data/tokenizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,811 copying build/lib/protenix/data/parser.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,815 copying build/lib/protenix/data/ccd.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,818 copying build/lib/protenix/data/substructure_perms.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,821 copying build/lib/protenix/data/data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,824 copying build/lib/protenix/data/featurizer.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,827 copying build/lib/protenix/data/json_maker.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,830 copying build/lib/protenix/data/infer_data_pipeline.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,833 copying build/lib/protenix/data/json_to_feature.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,835 copying build/lib/protenix/data/dataset.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,839 copying build/lib/protenix/data/msa_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,843 copying build/lib/protenix/data/dataloader.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,845 copying build/lib/protenix/data/filter.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,849 copying build/lib/protenix/data/constants.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,852 copying build/lib/protenix/data/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/data 2025-01-16T07:52:38,855 creating build/bdist.linux-armv7l/wheel/protenix/utils 2025-01-16T07:52:38,857 copying build/lib/protenix/utils/logger.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,859 copying build/lib/protenix/utils/torch_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,862 copying build/lib/protenix/utils/geometry.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,864 copying build/lib/protenix/utils/training.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,866 copying build/lib/protenix/utils/metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,869 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation 2025-01-16T07:52:38,870 copying build/lib/protenix/utils/permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-16T07:52:38,873 creating build/bdist.linux-armv7l/wheel/protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,875 copying build/lib/protenix/utils/permutation/chain_permutation/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,877 copying build/lib/protenix/utils/permutation/chain_permutation/pocket_based_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,880 copying build/lib/protenix/utils/permutation/chain_permutation/heuristic.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,883 copying build/lib/protenix/utils/permutation/chain_permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation/chain_permutation 2025-01-16T07:52:38,885 copying build/lib/protenix/utils/permutation/atom_permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-16T07:52:38,889 copying build/lib/protenix/utils/permutation/permutation.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-16T07:52:38,891 copying build/lib/protenix/utils/permutation/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils/permutation 2025-01-16T07:52:38,894 copying build/lib/protenix/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,896 copying build/lib/protenix/utils/file_io.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,898 copying build/lib/protenix/utils/distributed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,901 copying build/lib/protenix/utils/cropping.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,904 copying build/lib/protenix/utils/seed.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,906 copying build/lib/protenix/utils/lr_scheduler.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,908 copying build/lib/protenix/utils/scatter_utils.py -> build/bdist.linux-armv7l/wheel/./protenix/utils 2025-01-16T07:52:38,911 creating build/bdist.linux-armv7l/wheel/protenix/metrics 2025-01-16T07:52:38,913 copying build/lib/protenix/metrics/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-16T07:52:38,915 copying build/lib/protenix/metrics/rmsd.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-16T07:52:38,917 copying build/lib/protenix/metrics/lddt_metrics.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-16T07:52:38,920 copying build/lib/protenix/metrics/clash.py -> build/bdist.linux-armv7l/wheel/./protenix/metrics 2025-01-16T07:52:38,923 creating build/bdist.linux-armv7l/wheel/protenix/model 2025-01-16T07:52:38,924 copying build/lib/protenix/model/protenix.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,928 creating build/bdist.linux-armv7l/wheel/protenix/model/modules 2025-01-16T07:52:38,929 copying build/lib/protenix/model/modules/confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,932 copying build/lib/protenix/model/modules/transformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,935 copying build/lib/protenix/model/modules/embedders.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,938 copying build/lib/protenix/model/modules/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,940 copying build/lib/protenix/model/modules/diffusion.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,943 copying build/lib/protenix/model/modules/pairformer.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,946 copying build/lib/protenix/model/modules/frames.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,948 copying build/lib/protenix/model/modules/head.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,950 copying build/lib/protenix/model/modules/primitives.py -> build/bdist.linux-armv7l/wheel/./protenix/model/modules 2025-01-16T07:52:38,954 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm 2025-01-16T07:52:38,955 copying build/lib/protenix/model/layer_norm/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-16T07:52:38,958 copying build/lib/protenix/model/layer_norm/torch_ext_compile.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-16T07:52:38,961 creating build/bdist.linux-armv7l/wheel/protenix/model/layer_norm/kernel 2025-01-16T07:52:38,962 copying build/lib/protenix/model/layer_norm/kernel/compat.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-16T07:52:38,964 copying build/lib/protenix/model/layer_norm/kernel/type_shim.h -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-16T07:52:38,967 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda.cpp -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-16T07:52:38,970 copying build/lib/protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm/kernel 2025-01-16T07:52:38,974 copying build/lib/protenix/model/layer_norm/layer_norm.py -> build/bdist.linux-armv7l/wheel/./protenix/model/layer_norm 2025-01-16T07:52:38,976 copying build/lib/protenix/model/__init__.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,978 copying build/lib/protenix/model/loss.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,982 copying build/lib/protenix/model/generator.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,985 copying build/lib/protenix/model/sample_confidence.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,988 copying build/lib/protenix/model/utils.py -> build/bdist.linux-armv7l/wheel/./protenix/model 2025-01-16T07:52:38,991 creating build/bdist.linux-armv7l/wheel/configs 2025-01-16T07:52:38,993 copying build/lib/configs/__init__.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-16T07:52:38,994 copying build/lib/configs/configs_base.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-16T07:52:38,997 copying build/lib/configs/configs_inference.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-16T07:52:38,999 copying build/lib/configs/configs_data.py -> build/bdist.linux-armv7l/wheel/./configs 2025-01-16T07:52:39,002 running install_egg_info 2025-01-16T07:52:39,035 Copying protenix.egg-info to build/bdist.linux-armv7l/wheel/./protenix-0.4.0-py3.11.egg-info 2025-01-16T07:52:39,046 running install_scripts 2025-01-16T07:52:39,065 creating build/bdist.linux-armv7l/wheel/protenix-0.4.0.dist-info/WHEEL 2025-01-16T07:52:39,068 creating '/tmp/pip-wheel-6man6dli/protenix-0.4.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-01-16T07:52:39,070 adding 'configs/__init__.py' 2025-01-16T07:52:39,072 adding 'configs/configs_base.py' 2025-01-16T07:52:39,074 adding 'configs/configs_data.py' 2025-01-16T07:52:39,075 adding 'configs/configs_inference.py' 2025-01-16T07:52:39,076 adding 'protenix/__init__.py' 2025-01-16T07:52:39,078 adding 'protenix/config/__init__.py' 2025-01-16T07:52:39,080 adding 'protenix/config/config.py' 2025-01-16T07:52:39,081 adding 'protenix/config/extend_types.py' 2025-01-16T07:52:39,083 adding 'protenix/data/__init__.py' 2025-01-16T07:52:39,085 adding 'protenix/data/ccd.py' 2025-01-16T07:52:39,089 adding 'protenix/data/constants.py' 2025-01-16T07:52:39,091 adding 'protenix/data/data_pipeline.py' 2025-01-16T07:52:39,093 adding 'protenix/data/dataloader.py' 2025-01-16T07:52:39,098 adding 'protenix/data/dataset.py' 2025-01-16T07:52:39,102 adding 'protenix/data/featurizer.py' 2025-01-16T07:52:39,105 adding 'protenix/data/filter.py' 2025-01-16T07:52:39,107 adding 'protenix/data/infer_data_pipeline.py' 2025-01-16T07:52:39,109 adding 'protenix/data/json_maker.py' 2025-01-16T07:52:39,112 adding 'protenix/data/json_parser.py' 2025-01-16T07:52:39,114 adding 'protenix/data/json_to_feature.py' 2025-01-16T07:52:39,118 adding 'protenix/data/msa_featurizer.py' 2025-01-16T07:52:39,124 adding 'protenix/data/msa_utils.py' 2025-01-16T07:52:39,135 adding 'protenix/data/parser.py' 2025-01-16T07:52:39,138 adding 'protenix/data/substructure_perms.py' 2025-01-16T07:52:39,139 adding 'protenix/data/tokenizer.py' 2025-01-16T07:52:39,143 adding 'protenix/data/utils.py' 2025-01-16T07:52:39,144 adding 'protenix/metrics/__init__.py' 2025-01-16T07:52:39,146 adding 'protenix/metrics/clash.py' 2025-01-16T07:52:39,148 adding 'protenix/metrics/lddt_metrics.py' 2025-01-16T07:52:39,150 adding 'protenix/metrics/rmsd.py' 2025-01-16T07:52:39,152 adding 'protenix/model/__init__.py' 2025-01-16T07:52:39,154 adding 'protenix/model/generator.py' 2025-01-16T07:52:39,160 adding 'protenix/model/loss.py' 2025-01-16T07:52:39,163 adding 'protenix/model/protenix.py' 2025-01-16T07:52:39,166 adding 'protenix/model/sample_confidence.py' 2025-01-16T07:52:39,169 adding 'protenix/model/utils.py' 2025-01-16T07:52:39,170 adding 'protenix/model/layer_norm/__init__.py' 2025-01-16T07:52:39,172 adding 'protenix/model/layer_norm/layer_norm.py' 2025-01-16T07:52:39,173 adding 'protenix/model/layer_norm/torch_ext_compile.py' 2025-01-16T07:52:39,175 adding 'protenix/model/layer_norm/kernel/compat.h' 2025-01-16T07:52:39,176 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda.cpp' 2025-01-16T07:52:39,179 adding 'protenix/model/layer_norm/kernel/layer_norm_cuda_kernel.cu' 2025-01-16T07:52:39,180 adding 'protenix/model/layer_norm/kernel/type_shim.h' 2025-01-16T07:52:39,182 adding 'protenix/model/modules/__init__.py' 2025-01-16T07:52:39,184 adding 'protenix/model/modules/confidence.py' 2025-01-16T07:52:39,187 adding 'protenix/model/modules/diffusion.py' 2025-01-16T07:52:39,189 adding 'protenix/model/modules/embedders.py' 2025-01-16T07:52:39,190 adding 'protenix/model/modules/frames.py' 2025-01-16T07:52:39,191 adding 'protenix/model/modules/head.py' 2025-01-16T07:52:39,194 adding 'protenix/model/modules/pairformer.py' 2025-01-16T07:52:39,198 adding 'protenix/model/modules/primitives.py' 2025-01-16T07:52:39,202 adding 'protenix/model/modules/transformer.py' 2025-01-16T07:52:39,203 adding 'protenix/openfold_local/__init__.py' 2025-01-16T07:52:39,205 adding 'protenix/openfold_local/data/__init__.py' 2025-01-16T07:52:39,207 adding 'protenix/openfold_local/data/data_transforms.py' 2025-01-16T07:52:39,208 adding 'protenix/openfold_local/data/errors.py' 2025-01-16T07:52:39,211 adding 'protenix/openfold_local/data/mmcif_parsing.py' 2025-01-16T07:52:39,212 adding 'protenix/openfold_local/data/msa_identifiers.py' 2025-01-16T07:52:39,214 adding 'protenix/openfold_local/data/msa_pairing.py' 2025-01-16T07:52:39,218 adding 'protenix/openfold_local/data/parsers.py' 2025-01-16T07:52:39,221 adding 'protenix/openfold_local/data/templates.py' 2025-01-16T07:52:39,222 adding 'protenix/openfold_local/data/tools/__init__.py' 2025-01-16T07:52:39,224 adding 'protenix/openfold_local/data/tools/jackhmmer.py' 2025-01-16T07:52:39,225 adding 'protenix/openfold_local/data/tools/utils.py' 2025-01-16T07:52:39,227 adding 'protenix/openfold_local/model/__init__.py' 2025-01-16T07:52:39,228 adding 'protenix/openfold_local/model/dropout.py' 2025-01-16T07:52:39,230 adding 'protenix/openfold_local/model/outer_product_mean.py' 2025-01-16T07:52:39,233 adding 'protenix/openfold_local/model/primitives.py' 2025-01-16T07:52:39,234 adding 'protenix/openfold_local/model/triangular_attention.py' 2025-01-16T07:52:39,237 adding 'protenix/openfold_local/model/triangular_multiplicative_update.py' 2025-01-16T07:52:39,238 adding 'protenix/openfold_local/np/__init__.py' 2025-01-16T07:52:39,243 adding 'protenix/openfold_local/np/residue_constants.py' 2025-01-16T07:52:39,245 adding 'protenix/openfold_local/utils/__init__.py' 2025-01-16T07:52:39,248 adding 'protenix/openfold_local/utils/all_atom_multimer.py' 2025-01-16T07:52:39,249 adding 'protenix/openfold_local/utils/checkpointing.py' 2025-01-16T07:52:39,252 adding 'protenix/openfold_local/utils/chunk_utils.py' 2025-01-16T07:52:39,253 adding 'protenix/openfold_local/utils/feats.py' 2025-01-16T07:52:39,255 adding 'protenix/openfold_local/utils/precision_utils.py' 2025-01-16T07:52:39,259 adding 'protenix/openfold_local/utils/rigid_utils.py' 2025-01-16T07:52:39,261 adding 'protenix/openfold_local/utils/tensor_utils.py' 2025-01-16T07:52:39,263 adding 'protenix/openfold_local/utils/geometry/__init__.py' 2025-01-16T07:52:39,264 adding 'protenix/openfold_local/utils/geometry/quat_rigid.py' 2025-01-16T07:52:39,265 adding 'protenix/openfold_local/utils/geometry/rigid_matrix_vector.py' 2025-01-16T07:52:39,267 adding 'protenix/openfold_local/utils/geometry/rotation_matrix.py' 2025-01-16T07:52:39,268 adding 'protenix/openfold_local/utils/geometry/test_utils.py' 2025-01-16T07:52:39,269 adding 'protenix/openfold_local/utils/geometry/utils.py' 2025-01-16T07:52:39,271 adding 'protenix/openfold_local/utils/geometry/vector.py' 2025-01-16T07:52:39,273 adding 'protenix/openfold_local/utils/kernel/__init__.py' 2025-01-16T07:52:39,274 adding 'protenix/openfold_local/utils/kernel/attention_core.py' 2025-01-16T07:52:39,276 adding 'protenix/utils/__init__.py' 2025-01-16T07:52:39,279 adding 'protenix/utils/cropping.py' 2025-01-16T07:52:39,281 adding 'protenix/utils/distributed.py' 2025-01-16T07:52:39,282 adding 'protenix/utils/file_io.py' 2025-01-16T07:52:39,284 adding 'protenix/utils/geometry.py' 2025-01-16T07:52:39,285 adding 'protenix/utils/logger.py' 2025-01-16T07:52:39,287 adding 'protenix/utils/lr_scheduler.py' 2025-01-16T07:52:39,288 adding 'protenix/utils/metrics.py' 2025-01-16T07:52:39,290 adding 'protenix/utils/scatter_utils.py' 2025-01-16T07:52:39,291 adding 'protenix/utils/seed.py' 2025-01-16T07:52:39,293 adding 'protenix/utils/torch_utils.py' 2025-01-16T07:52:39,294 adding 'protenix/utils/training.py' 2025-01-16T07:52:39,296 adding 'protenix/utils/permutation/__init__.py' 2025-01-16T07:52:39,300 adding 'protenix/utils/permutation/atom_permutation.py' 2025-01-16T07:52:39,302 adding 'protenix/utils/permutation/permutation.py' 2025-01-16T07:52:39,304 adding 'protenix/utils/permutation/utils.py' 2025-01-16T07:52:39,306 adding 'protenix/utils/permutation/chain_permutation/__init__.py' 2025-01-16T07:52:39,310 adding 'protenix/utils/permutation/chain_permutation/heuristic.py' 2025-01-16T07:52:39,312 adding 'protenix/utils/permutation/chain_permutation/pocket_based_permutation.py' 2025-01-16T07:52:39,313 adding 'protenix/utils/permutation/chain_permutation/utils.py' 2025-01-16T07:52:39,315 adding 'protenix/web_service/__init__.py' 2025-01-16T07:52:39,317 adding 'protenix/web_service/colab_request_parser.py' 2025-01-16T07:52:39,319 adding 'protenix/web_service/colab_request_utils.py' 2025-01-16T07:52:39,320 adding 'protenix/web_service/dependency_url.py' 2025-01-16T07:52:39,322 adding 'protenix/web_service/prediction_visualization.py' 2025-01-16T07:52:39,324 adding 'protenix/web_service/viewer.py' 2025-01-16T07:52:39,327 adding 'runner/__init__.py' 2025-01-16T07:52:39,329 adding 'runner/batch_inference.py' 2025-01-16T07:52:39,330 adding 'runner/dumper.py' 2025-01-16T07:52:39,332 adding 'runner/ema.py' 2025-01-16T07:52:39,334 adding 'runner/inference.py' 2025-01-16T07:52:39,335 adding 'runner/msa_search.py' 2025-01-16T07:52:39,339 adding 'runner/train.py' 2025-01-16T07:52:39,340 adding 'scripts/__init__.py' 2025-01-16T07:52:39,342 adding 'scripts/colabfold_msa.py' 2025-01-16T07:52:39,344 adding 'scripts/gen_ccd_cache.py' 2025-01-16T07:52:39,345 adding 'scripts/prepare_training_data.py' 2025-01-16T07:52:39,348 adding 'scripts/msa/step1-get_prot_seq.py' 2025-01-16T07:52:39,349 adding 'scripts/msa/step2-get_msa.ipynb' 2025-01-16T07:52:39,351 adding 'scripts/msa/step3-uniref_add_taxid.py' 2025-01-16T07:52:39,352 adding 'scripts/msa/step4-split_msa_to_uniref_and_others.py' 2025-01-16T07:52:39,354 adding 'protenix-0.4.0.dist-info/LICENSE' 2025-01-16T07:52:39,355 adding 'protenix-0.4.0.dist-info/METADATA' 2025-01-16T07:52:39,356 adding 'protenix-0.4.0.dist-info/WHEEL' 2025-01-16T07:52:39,357 adding 'protenix-0.4.0.dist-info/entry_points.txt' 2025-01-16T07:52:39,358 adding 'protenix-0.4.0.dist-info/top_level.txt' 2025-01-16T07:52:39,360 adding 'protenix-0.4.0.dist-info/RECORD' 2025-01-16T07:52:39,368 removing build/bdist.linux-armv7l/wheel 2025-01-16T07:52:39,517 Building wheel for protenix (setup.py): finished with status 'done' 2025-01-16T07:52:39,524 Created wheel for protenix: filename=protenix-0.4.0-py3-none-any.whl size=418105 sha256=0ed805ac2fa5dd681d530b84f093142316ea67bd9fba6b63f374d7ec3490756f 2025-01-16T07:52:39,525 Stored in directory: /tmp/pip-ephem-wheel-cache-edgyjoo5/wheels/6a/99/4b/99f00d221c318c4d8dcd27773f6d58a7e06542d6515534729b 2025-01-16T07:52:39,539 Successfully built protenix 2025-01-16T07:52:39,553 Removed build tracker: '/tmp/pip-build-tracker-j7bs27nz'